diff --git a/vignettes/getting-started.Rmd b/vignettes/getting-started.Rmd index 8926f94..507d675 100644 --- a/vignettes/getting-started.Rmd +++ b/vignettes/getting-started.Rmd @@ -30,7 +30,10 @@ Let's examine this example pgPEN counts table. It's divided into columns contain - `id`: an ID corresponding to the names of paired guides - `seq_1`: gRNA sequence 1, targeting "paralog A" - `seq_2`: gRNA sequence 2, targeting "paralog B" -- The sample, day, and replicate number for which gRNAs were sequenced (TODO) +- `Day00_RepA`: Gene Counts from Day 00 for Replicate A +- `Day05_RepA`: Gene Counts from Day 05 for Replicate A +- `Day22_RepA`: Gene Counts from Day 22 for Replicate A +- `Day22_RepB`: Gene Counts from Day 22 for Replicate B ```{r} example_data <- gimap::example_data() @@ -86,6 +89,14 @@ gimap_dataset <- gimap::setup_data(counts = example_counts, You'll notice that this set up gives us a list of formatted data. This contains the original counts we gave `setup_data()` function but also normalized counts, and the total counts per sample. +- Raw counts: Original data +- Counts per Sample: Add up all the counts for each sample +- Transformed data: Contains normalized counts, counts per million (cpm) +- Log2 CPM: log-2 transformed CPM +- pg_metadata: paired guide metadata +- sample_metadata: Metadata of dataset where columns are different samples and rows are different paired guide. + + ```{r} str(gimap_dataset)